2006–2011: Ys and Have One on Me
Her second album, Ys (), was released in November 2006, also by Drag City. The album features orchestrations and arrangements by Van Dyke Parks, engineering from Steve Albini and mixing by Drag City label-mate Jim O'Rourke. On a road trip, Bill Callahan recommended she listen to the album Song Cycle by Parks, which led to him being chosen to arrange her work on Ys. To support Ys, Newsom performed the album live in 2008 with the Brooklyn Philharmonic in New York City and with the Sydney Symphony Orchestra in Sydney, Australia. Ys garnered Newsom wider exposure, charting at number 134 on the Billboard 200. The album was also nominated for a 2007 Shortlist Music Prize. As of 2010, Ys had sold 250,000 copies.
In 2009, she appeared in the music video for the song "Kids" by the group MGMT. Also in 2009, Newsom appeared as a guest harpist on the Moore Brothers' album Aptos and played piano on Golden Shoulders' Get Reasonable. Newsom provided additional vocals for The Lonely Island's song "Ras Trent" during this period as well. On March 28, 2009, she performed over two hours of new material at an unannounced concert in Big Sur, California, with fellow Nevada City singer-lyricist Mariee Sioux under the pseudonym the Beatles's. Those in attendance reported that about one-third of her new material was played primarily on piano, with a backing arrangement of banjo, violin, guitar and drums. On February 11, 2010, Pitchfork Media reported that Newsom would be the subject of a tribute book titled Visions of Joanna Newsom which was published by Roan Press and features a contribution from author and publisher Dave Eggers.
Newsom's third studio album, Have One on Me, was released on February 23, 2010, in North America. A triple album recorded in Tokyo in 2009, it consists of over two hours of songs. Writing for the Los Angeles Times, Ann Powers praised the album's variety, adding: "Newsom uses the songwriter's default mode to explore how traditional love, for women, can be both the beginning and the end of possibility: a way to escape home and be exiled from it; to welcome children or be burdened by fertility; to be entrusted with secrets, or betrayed." Throughout 2010, she toured Europe and North America to promote the record, supported by a five-piece band, and also appeared as a guest composer on the album How I Got Over by the Roots, released in June of that year. She was also selected by Matt Groening to perform at the edition of the All Tomorrow's Parties festival he curated in May 2010 in Minehead, England. In December 2010, a tribute album of Newsom covers was released as a digital download. Artists involved include M. Ward, Billy Bragg, Francesco Santocono, Guy Buttery and Owen Pallett, with all proceeds going to Oxfam America's Pakistan Flood Relief Efforts.
On July 19, 2011, Newsom's second single, "What We Have Known," was released on 12" vinyl. The single was originally the b-side to her first single, "Sprout and the Bean". In June 2011, she filmed her second music video (for the song "Good Intentions Paving Company") with directors Karni & Saul. Newsom was selected by Jeff Mangum of Neutral Milk Hotel to perform at the All Tomorrow's Parties festival that he curated in March 2012 in Minehead, England. In late 2011, Newsom contributed vocals to "The Muppet Show Theme" for The Muppets and appeared on the cover of the 10th anniversary issue of Under the Radar with Robin Pecknold.